Summary1. While phylogenies have been getting easier to build, it has been difficult to reuse, combine and synthesize the information they provide because published trees are often only available as image files, and taxonomic information is not standardized across studies. 2. The Open Tree of Life (OTL) project addresses these issues by providing a digital tree that encompasses all organisms, built by combining taxonomic information and published phylogenies. The project also provides tools and services to query and download parts of this synthetic tree, as well as the source data used to build it. Here, we present rotl, an R package to search and download data from the Open Tree of Life directly in R. 3. rotl uses common data structures allowing researchers to take advantage of the rich set of tools and methods that are available in R to manipulate, analyse and visualize phylogenies. Here, and in the vignettes accompanying the package, we demonstrate how rotl can be used with other R packages to analyse biodiversity data. 4. As phylogenies are being used in a growing number of applications, rotl facilitates access to phylogenetic data and allows their integration with statistical methods and data sources available in R.Key-words: comparative methods, macroevolution, Open Tree of Life, phylogenetics Advances in sequencing and computing technologies have lead to a revolution in systematic biology. The ability to routinely generate molecular data sets from any extant organism has allowed researchers to resolve long-standing taxonomic disputes and estimate phylogenies for previously understudied groups. In parallel, the ease with which phylogenies can be estimated has spurred the development of new phylogenetic comparative methods. These methods allow researchers to explore fundamental questions about the origin of biodiversity including the evolution of morphological and ecological traits, the spatiotemporal variation in speciation rates, or both (O'Meara 2012;Pennell & Harmon 2013).Ideally, the ever increasing number of published phylogenies would contribute to a synthesis of phylogenetic knowledge, ultimately leading to a better understanding of the history of life while at the same time providing high-quality phylogenetic information for use in comparative analyses. However, in practice, synthesizing phylogenetic data is a difficult task. Phylogenetic information is largely scattered, often only available as image files within publications, and the lack of standardization to store and represent phylogenetic data makes it difficult for researchers to access, synthesize and integrate this information into their own research (Stoltzfus et al. 2012;Drew et al. 2013;Magee, May & Moore 2014; but see Cranston et al. 2014 for suggestions of best practices).The Open Tree of Life (OTL) project aims at assembling and synthesizing our current understanding of phylogenetic relationships across all organisms on Earth while providing tools and services that facilitate access to this information (Hinchliff et al. 2015). OTL ...

MMOD is a library for the R programming language that allows the calculation of the population differentiation measures D(est), G″(ST) and φ'(ST). R provides a powerful environment in which to conduct and record population genetic analyses but, at present, no R libraries provide functions for the calculation of these statistics from standard population genetic files. In addition to the calculation of differentiation measures, mmod can produce parametric bootstrap and jackknife samples of data sets for further analysis. By integrating with and complimenting the existing libraries adegenet and pegas, mmod extends the power of R as a population genetic platform.

Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C data to examine the three-dimensional organisation of the genome, and RNA-seq data to investigate how Epichloë genome structure contributes to the suite of transcriptional changes needed to maintain symbiotic relationships with the grass host. Our results reveal a genome in which very repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences that are almost repeat-free. In contrast to other species reported to date, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.

The stunting effect of ocean acidification on development of calcifying invertebrate larvae has emerged as a significant effect of global change. We assessed the arm growth response of sea urchin echinoplutei, here used as a proxy of larval calcification, to increased seawater acidity/ p CO 2 and decreased carbonate mineral saturation in a global synthesis of data from 15 species. Phylogenetic relatedness did not influence the observed patterns. Regardless of habitat or latitude, ocean acidification impedes larval growth with a negative relationship between arm length and increased acidity/ p CO 2 and decreased carbonate mineral saturation. In multiple linear regression models incorporating these highly correlated parameters, p CO 2 exerted the greatest influence on decreased arm growth in the global dataset and also in the data subsets for polar and subtidal species. Thus, reduced growth appears largely driven by organism hypercapnia. For tropical species, decreased carbonate mineral saturation was most important. No single parameter played a dominant role in arm size reduction in the temperate species. For intertidal species, the models were equivocal. Levels of acidification causing a significant (approx. 10–20+%) reduction in arm growth varied between species. In 13 species, reduction in length of arms and supporting skeletal rods was evident in larvae reared in near-future ( p CO 2 800+ µatm) conditions, whereas greater acidification ( p CO 2 1000+ µatm) reduced growth in all species. Although multi-stressor studies are few, when temperature is added to the stressor mix, near-future warming can reduce the negative effect of acidification on larval growth. Broadly speaking, responses of larvae from across world regions showed similar trends despite disparate phylogeny, environments and ecology. Larval success may be the bottleneck for species success with flow-on effects for sea urchin populations and marine ecosystems.